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This paper presents a part-of-speech tagger which is specifically tuned for biomedical text. We have built the tagger with maximum entropy modeling and a state-of-the-art tagging algorithm. The tagger was trained on a corpus containing newspaper articles and biomedical documents so that it would work well on various types of biomedical text. Experimental(More)
This paper presents a bidirectional inference algorithm for sequence labeling problems such as part-of-speech tagging , named entity recognition and text chunking. The algorithm can enumerate all possible decomposition structures and find the highest probability sequence together with the corresponding decomposition structure in polynomial time. We also(More)
This paper presents a simple yet effective semi-supervised method to improve Chi-nese word segmentation and POS tagging. We introduce novel features derived from large auto-analyzed data to enhance a simple pipelined system. The auto-analyzed data are generated from unlabeled data by using a baseline system. We evaluate the usefulness of our approach in a(More)
Conventional approaches to Chinese word segmentation treat the problem as a character-based tagging task. Recently, semi-Markov models have been applied to the problem, incorporating features based on complete words. In this paper, we propose an alternative, a latent variable model, which uses hybrid information based on both word sequences and character(More)
Stochastic gradient descent (SGD) uses approximate gradients estimated from subsets of the training data and updates the parameters in an online fashion. This learning framework is attractive because it often requires much less training time in practice than batch training algorithms. However, L1-regularization, which is becoming popular in natural language(More)
This paper presents a machine learning approach to acronym generation. We formalize the generation process as a sequence labeling problem on the letters in the definition (expanded form) so that a variety of Markov modeling approaches can be applied to this task. To construct the data for training and testing, we extracted acronym-definition pairs from(More)
We describe a system that extracts disease-gene relations from Medline. We constructed a dictionary for disease and gene names from six public databases and extracted relation candidates by dictionary matching. Since dictionary matching produces a large number of false positives, we developed a method of machine learning-based named entity recognition (NER)(More)
MOTIVATION One of the bottlenecks of biomedical data integration is variation of terms. Exact string matching often fails to associate a name with its biological concept, i.e. ID or accession number in the database, due to seemingly small differences of names. Soft string matching potentially enables us to find the relevant ID by considering the similarity(More)
This paper presents techniques to apply semi-CRFs to Named Entity Recognition tasks with a tractable computational cost. Our framework can handle an NER task that has long named entities and many labels which increase the computational cost. To reduce the computational cost, we propose two techniques: the first is the use of feature forests, which enables(More)
This paper shows that the performance of history-based models can be significantly improved by performing lookahead in the state space when making each classification decision. Instead of simply using the best action output by the classifier, we determine the best action by looking into possible sequences of future actions and evaluating the final states(More)